Merge pull request #2 from tomography/master

resync

.travis.yml

@@ -8,7 +8,8 @@ python:
 os:
   - linux
 
-sudo: false
+sudo: required
+dist: trusty
 
 before_script:
   - "export DISPLAY=:99.0"
@@ -29,8 +30,8 @@ before_install:
   - conda install anaconda-client
 
 install:
-  - conda install python=$TRAVIS_PYTHON_VERSION nose six numpy scipy matplotlib python-coveralls pillow cached-property
-  - pip install phasepack
+  - conda install python=$TRAVIS_PYTHON_VERSION nose six numpy scipy matplotlib python-coveralls pillow cached-property setuptools
+  - pip install phasepack polytope
   - conda info -a
   - python setup.py build_ext --inplace
 

docs/source/conf.py

@@ -341,9 +341,10 @@ def __getattr__(cls, name):
             return Mock()
 
 MOCK_MODULES = [
-    'numpy', 'scipy', 'scipy.stats', 'scipy.ndimage', 
-    'matplotlib', 'matplotlib.pyplot', 'matplotlib.patches', 
-    'phasepack', 'cached-property']
+    'numpy', 'scipy', 'scipy.stats', 'scipy.ndimage',
+    'matplotlib', 'matplotlib.pyplot', 'matplotlib.patches',
+    'phasepack', 'cached-property', 'matplotlib.path',
+    'matplotlib.patheffects', 'matplotlib.axis', 'scipy.spatial']
 
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = Mock()

meta.yaml

@@ -15,12 +15,13 @@ requirements:
 
   run:
     - python
-    - numpy    
+    - numpy
     - scipy
     - six
     - matplotlib
     - phasepack
     - cached-property
+    - polytope
 
 test:
   # Python imports

requirements-doc.txt

@@ -1,2 +1,3 @@
 sphinx
+sphinx_rtd_theme
 sphinxcontrib-bibtex

setup.py

@@ -49,7 +49,7 @@
 import setuptools
 from version_hashtag import append_dev_info
 
-version_info = (0, 1, 0)
+version_info = (0, 2, 0)
 version = '.'.join([str(x) for x in version_info])
 version = append_dev_info(version)
 with open('VERSION', 'w') as f:

tests/test_acquisition.py

@@ -0,0 +1,18 @@
+from __future__ import (absolute_import, division, print_function,
+                        unicode_literals)
+
+from xdesign.acquisition import raster_scan
+from numpy.testing import assert_allclose, assert_raises, assert_equal
+import numpy as np
+
+
+def test_raster_scan():
+    positions = [p.numpy.flatten() for p in raster_scan(2, 2)]
+    positions = np.hstack(np.hstack(positions))
+
+    correct = np.array([0.25,  -10., 0.25,       10.,
+                        0.75,  -10., 0.75,       10.,
+                        11.,   0.25,   -9.,     0.25,
+                        11.,   0.75,   -9.,     0.75])
+
+    assert_allclose(positions, correct)

tests/test_geometry.py

@@ -50,7 +50,7 @@
                         unicode_literals)
 
 from xdesign.geometry import *
-from xdesign.geometry import beamcirc
+from xdesign.geometry import beamcirc, beampoly
 from xdesign.acquisition import *
 from numpy.testing import assert_allclose, assert_raises, assert_equal
 import numpy as np
@@ -61,125 +61,208 @@
 __docformat__ = 'restructuredtext en'
 
 
+# Transformations
+
+def rotate_around_self():
+    P0 = Point([0, 0])
+    origin = P0
+    P1 = rotate(P0, np.pi/2, origin)
+    assert_allclose([P1.x, P1.y], [0, 0])
+
+
+def rotate_around_other():
+    P0 = Point([0, 0])
+    origin = Point([1, 0])
+    P1 = rotate(P0, np.pi/2, origin)
+    assert_allclose([P1.x, P1.y], [1, -1])
+
+
+def test_Point_rotate_around_self():
+    P0 = Point([0, 0])
+    origin = P0
+    P0.rotate(np.pi/2, origin)
+    assert_allclose([P0.x, P0.y], [0, 0])
+
+
+def test_Point_rotate_around_other():
+    P0 = Point([0, 0])
+    origin = Point([1, 0])
+    P0.rotate(np.pi/2, origin)
+    assert_allclose([P0.x, P0.y], [1, -1])
+
+    P0 = Point([0, 0])
+    origin = Point([0, 1])
+    P0.rotate(np.pi/2, origin)
+    assert_allclose([P0.x, P0.y], [1, 1])
+
+    P0 = Point([0, 0])
+    origin = Point([-1, 0])
+    P0.rotate(np.pi/2, origin)
+    assert_allclose([P0.x, P0.y], [-1, 1])
+
+    P0 = Point([0, 0])
+    origin = Point([-1, -1])
+    P0.rotate(np.pi/2, origin)
+    assert_allclose([P0.x, P0.y], [-2, 0])
+
+
+def test_translate():
+    P0 = Point([0, 0])
+    P0.translate([2.3, 4.5])
+    assert_equal([P0.x, P0.y], [2.3, 4.5])
+
+
 # Nonintersecting beams
 
 def test_beamcirc_nonintersecting_top():
-    circ = Circle(Point(0, 3), 1)
-    beam = Beam(Point(-2, 0), Point(2, 0), 2)
+    circ = Circle(Point([0, 3]), 1)
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 2)
     assert_allclose(beamcirc(beam, circ), 0., rtol=1e-6)
 
 
 def test_beamcirc_nonintersecting_bottom():
-    circ = Circle(Point(0, -3), 1)
-    beam = Beam(Point(-2, 0), Point(2, 0), 2)
+    circ = Circle(Point([0, -3]), 1)
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 2)
     assert_allclose(beamcirc(beam, circ), 0., rtol=1e-6)
 
 
+def test_beampoly_nonintersecting_top():
+    tri = Triangle(Point([0, 1]), Point([1, -1]), Point([-1, -1]))
+    beam = Beam(Point([-2, 2]), Point([2, 2]), 2)
+    assert_allclose(beampoly(beam, tri), 0., rtol=1e-6)
+
+
+def test_beampoly_nonintersecting_bottom():
+    tri = Triangle(Point([0, 1]), Point([1, -1]), Point([-1, -1]))
+    beam = Beam(Point([-2, -2]), Point([2, -2]), 2)
+    assert_allclose(beampoly(beam, tri), 0., rtol=1e-6)
+
+
 # Partial intersections
 
 def test_beamcirc_intersecting_partially_from_top_outside_center():
-    circ = Circle(Point(0, 1.5), 1)
-    beam = Beam(Point(-2, 0), Point(2, 0), 2)
+    circ = Circle(Point([0, 1.5]), 1)
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 2)
     assert_allclose(beamcirc(beam, circ), 0.614184849304, rtol=1e-6)
 
 
 def test_beamcirc_intersecting_partially_from_bottom_outside_center():
-    circ = Circle(Point(0, -1.5), 1)
-    beam = Beam(Point(-2, 0), Point(2, 0), 2)
+    circ = Circle(Point([0, -1.5]), 1)
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 2)
     assert_allclose(beamcirc(beam, circ), 0.614184849304, rtol=1e-6)
 
 
 def test_beamcirc_intersecting_partially_from_top_inside_center():
-    circ = Circle(Point(0, 0.5), 1)
-    beam = Beam(Point(-2, 0), Point(2, 0), 2)
+    circ = Circle(Point([0, 0.5]), 1)
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 2)
     assert_allclose(beamcirc(beam, circ), 2.52740780429, rtol=1e-6)
 
 
 def test_beamcirc_intersecting_partially_from_bottom_inside_center():
-    circ = Circle(Point(0, -0.5), 1)
-    beam = Beam(Point(-2, 0), Point(2, 0), 2)
+    circ = Circle(Point([0, -0.5]), 1)
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 2)
     assert_allclose(beamcirc(beam, circ), 2.52740780429, rtol=1e-6)
 
 
+def test_beampoly_intersecting_partially_from_top():
+    tri = Rectangle(Point([0, 0]), Point([1, 0]), Point([1, 1]), Point([0, 1]))
+    beam = Beam(Point([-2, 1]), Point([2, 1]), 1)
+    assert_allclose(beampoly(beam, tri), 1/2, rtol=1e-6)
+
+
+def test_beampoly_intersecting_partially_from_bottom():
+    tri = Rectangle(Point([0, 0]), Point([1, 0]), Point([1, 1]), Point([0, 1]))
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 1)
+    assert_allclose(beampoly(beam, tri), 1/2, rtol=1e-6)
+
+
 # Full intersections
 
 def test_beamcirc_intersecting_fully_from_top_outside_center():
-    circ = Circle(Point(0, 1.5), 3)
-    beam = Beam(Point(-2, 0), Point(2, 0), 2)
+    circ = Circle(Point([0, 1.5]), 3)
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 2)
     assert_allclose(beamcirc(beam, circ), 10.0257253792, rtol=1e-6)
 
 
 def test_beamcirc_intersecting_fully_from_bottom_outside_center():
-    circ = Circle(Point(0, -1.5), 3)
-    beam = Beam(Point(-2, 0), Point(2, 0), 2)
+    circ = Circle(Point([0, -1.5]), 3)
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 2)
     assert_allclose(beamcirc(beam, circ), 10.0257253792, rtol=1e-6)
 
 
 def test_beamcirc_intersecting_fully_from_top_inside_center():
-    circ = Circle(Point(0, 0.5), 3)
-    beam = Beam(Point(-2, 0), Point(2, 0), 2)
+    circ = Circle(Point([0, 0.5]), 3)
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 2)
     assert_allclose(beamcirc(beam, circ), 11.5955559562, rtol=1e-6)
 
 
 def test_beamcirc_intersecting_fully_from_bottom_inside_center():
-    circ = Circle(Point(0, -0.5), 3)
-    beam = Beam(Point(-2, 0), Point(2, 0), 2)
+    circ = Circle(Point([0, -0.5]), 3)
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 2)
     assert_allclose(beamcirc(beam, circ), 11.5955559562, rtol=1e-6)
 
 
 def test_beamcirc_intersecting_fully():
-    circ = Circle(Point(0, 0), 1)
-    beam = Beam(Point(-2, 0), Point(2, 0), 2)
+    circ = Circle(Point([0, 0]), 1)
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 2)
     assert_allclose(beamcirc(beam, circ), 3.14159265359, rtol=1e-6)
 
+def test_beampoly_intersecting_fully():
+    tri = Rectangle(Point([-1, -1]), Point([1, -1]), Point([1, 1]), Point([-1, 1]))
+    beam = Beam(Point([-2, 0]), Point([2, 0]), 3)
+    assert_allclose(beampoly(beam, tri), 4, rtol=1e-6)
 
 # Vertical intersection.
 
 def test_beamcirc_vertical_intersection():
-    circ = Circle(Point(0, 0), 1)
-    beam = Beam(Point(-1, -1), Point(1, 1), 1)
+    circ = Circle(Point([0, 0]), 1)
+    beam = Beam(Point([-1, -1]), Point([1, 1]), 1)
     assert_allclose(beamcirc(beam, circ), 1.91322295498, rtol=1e-6)
 
+def test_beampoly_vertical_intersection():
+    tri = Rectangle(Point([-5, 0]), Point([5, 0]), Point([5, 1]), Point([-5, 1]))
+    beam = Beam(Point([0, -1]), Point([0, 1]), 1)
+    assert_allclose(beampoly(beam, tri), 1, rtol=1e-6)
 
 # Line
 
 def test_Line_slope_vertical():
-    line = Line(Point(0, -1), Point(0, 1))
+    line = Line(Point([0, -1]), Point([0, 1]))
     assert_allclose(line.slope, np.inf, rtol=1e-6)
 
 
 def test_Line_yintercept_vertical():
-    line = Line(Point(0, -1), Point(0, 1))
-    assert_allclose(line.yintercept, 0, rtol=1e-6)
+    line = Line(Point([0, -1]), Point([0, 1]))
+    assert_allclose(line.yintercept, np.inf, rtol=1e-6)
 
 
 def test_Line_slope():
-    line = Line(Point(-1, 0), Point(1, 2))
+    line = Line(Point([-1, 0]), Point([1, 2]))
     assert_allclose(line.slope, 1, rtol=1e-6)
 
 
 def test_Line_yintercept():
-    line = Line(Point(-1, 0), Point(1, 2))
+    line = Line(Point([-1, 0]), Point([1, 2]))
     assert_allclose(line.yintercept, 1, rtol=1e-6)
 
 
 def test_Line_same_points():
-    assert_raises(ValueError, Line, Point(1, 2), Point(1, 2))
+    assert_raises(ValueError, Line, Point([1, 2]), Point([1, 2]))
 
 
 # Circle
 
 def test_Circle_area():
-    circle = Circle(Point(0, 0), 1)
+    circle = Circle(Point([0, 0]), 1)
     assert_allclose(circle.area, 3.14159265359, rtol=1e-6)
 
 
 def test_Mesh_area():
-    p5 = Point(0, 0)
-    p1 = Point(1, 1)
-    p4 = Point(1, -1)
-    p3 = Point(-1, -1)
-    p2 = Point(-1, 1)
+    p5 = Point([0, 0])
+    p1 = Point([1, 1])
+    p4 = Point([1, -1])
+    p3 = Point([-1, -1])
+    p2 = Point([-1, 1])
     m = Mesh()
     assert_equal(m.area, 0)
     m.append(Triangle(p5, p1, p2))
@@ -190,25 +273,25 @@ def test_Mesh_area():
 
 
 def test_Mesh_center():
-    p5 = Point(0, 0)
-    p1 = Point(1, 1)
-    p4 = Point(1, -1)
-    p3 = Point(-1, -1)
-    p2 = Point(-1, 1)
+    p5 = Point([0, 0])
+    p1 = Point([1, 1])
+    p4 = Point([1, -1])
+    p3 = Point([-1, -1])
+    p2 = Point([-1, 1])
     m = Mesh()
-    assert_equal(m.center, Point(0, 0))
+    assert_equal(m.center, Point([0, 0]))
 
     m.append(Triangle(p5, p1, p2))
     m.append(Triangle(p5, p2, p3))
     m.append(Triangle(p5, p3, p4))
     m.append(Triangle(p5, p4, p1))
-    assert_equal(m.center, Point(0, 0))
+    assert_equal(m.center, Point([0, 0]))
 
     m.pop()
     m.pop()
     m.pop()
     m.pop()
-    assert_equal(m.center, Point(0, 0))
+    assert_equal(m.center, Point([0, 0]))
 
 
 if __name__ == '__main__':